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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0723

PubMed

38179933, Appl Environ Microbiol. 2024 Jan 24;90(1):e0176823. doi: 10.1128/aem.01768-23. Epub 2024 Jan 5.

Characterization method

crystallization,high-performance anion-exchange chromatography,enzyme activity assay

Genomic accession number

NZ_DS995531.1

Nucelotide position range

42179-73562

Substrate

pectin

Loci

BACDOR_RS19925-BACDOR_RS19845

Species

Phocaeicola dorei DSM 17855/357276

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BACDOR_RS19925 WP_007831510.1 0 - 2763 (-) NZ_DS995531.1:42179-44942 -
- BACDOR_RS19920 WP_007831516.1 2775 - 4203 (-) NZ_DS995531.1:44954-46382 3.2.1.-
- BACDOR_RS19915 WP_007831518.1 4218 - 5022 (-) NZ_DS995531.1:46397-47201 -
- BACDOR_RS19910 WP_007831519.1 5018 - 5717 (-) NZ_DS995531.1:47197-47896 -
- BACDOR_RS19905 WP_007831520.1 5694 - 7179 (-) NZ_DS995531.1:47873-49358 3.2.1.-
- BACDOR_RS19900 WP_007831521.1 7196 - 8471 (-) NZ_DS995531.1:49375-50650 -
- BACDOR_RS19895 WP_007831522.1 8489 - 11357 (-) NZ_DS995531.1:50668-53536 -
- BACDOR_RS19890 WP_007831524.1 11568 - 13923 (+) NZ_DS995531.1:53747-56102 -
- BACDOR_RS19885 WP_007831526.1 13901 - 16016 (+) NZ_DS995531.1:56080-58195 3.2.1.23
- BACDOR_RS19880 WP_371741508.1 16134 - 17265 (-) NZ_DS995531.1:58313-59444 -
- BACDOR_RS19875 WP_007831530.1 17408 - 20696 (-) NZ_DS995531.1:59587-62875 -
- BACDOR_RS19870 WP_007831532.1 20809 - 22663 (-) NZ_DS995531.1:62988-64842 -
- BACDOR_RS19865 WP_007831539.1 22678 - 23962 (-) NZ_DS995531.1:64857-66141 3.-.-.-
- BACDOR_RS19860 WP_007831541.1 24004 - 25786 (-) NZ_DS995531.1:66183-67965 -
- BACDOR_RS19855 WP_007831547.1 26028 - 26346 (-) NZ_DS995531.1:68207-68525 -
- BACDOR_RS19850 WP_007831550.1 26436 - 28575 (-) NZ_DS995531.1:68615-70754 -
- BACDOR_RS19845 WP_007831557.1 28606 - 31384 (-) NZ_DS995531.1:70785-73563 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2763 (-) CAZyme: GH106 Yes
- 2776 - 4203 (-) CAZyme: GH28 Yes
- 4219 - 5022 (-) other Yes
- 5019 - 5717 (-) other Yes
- 5695 - 7179 (-) CAZyme: GH28 Yes
- 7197 - 8471 (-) CAZyme: CE12 Yes
- 8490 - 11357 (-) CAZyme: GH2 Yes
- 11569 - 13923 (+) CAZyme: GH43_18|GH43_34|CBM32 Yes
- 13902 - 16016 (+) CAZyme: GH42 Yes
- 16135 - 17265 (-) CAZyme: GH105 Yes
- 17409 - 20696 (-) CAZyme: GH106|GH28 Yes
- 20810 - 22663 (-) CAZyme: PL11 Yes
- 22679 - 23962 (-) CAZyme: CE15 Yes
- 24005 - 25786 (-) CAZyme: GH78 Yes
- 26029 - 26346 (-) other Yes
- 26437 - 28575 (-) other Yes
- 28607 - 31384 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

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PUL ID

PUL0723

PubMed

38179933, Appl Environ Microbiol. 2024 Jan 24;90(1):e0176823. doi: 10.1128/aem.01768-23. Epub 2024 Jan 5.

Title

Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds.

Author

Seveso A, Mazurkewich S, Banerjee S, Poulsen J-CN, Lo Leggio L, Larsbrink J

Abstract

Lignocellulose is a renewable but complex material exhibiting high recalcitrance to enzymatic hydrolysis, which is attributed, in part, to the presence of covalent linkages between lignin and polysaccharides in the plant cell wall. Glucuronoyl esterases from carbohydrate esterase family 15 (CE15) have been proposed as an aid in reducing this recalcitrance by cleaving ester bonds found between lignin and glucuronoxylan. In the Bacteroidota phylum, some species organize genes related to carbohydrate metabolism in polysaccharide utilization loci (PULs) which encode all necessary proteins to bind, deconstruct, and respond to a target glycan. Bioinformatic analyses identified CE15 members in some PULs that appear to not target the expected glucuronoxylan. Here, five CE15 members from such PULs were investigated with the aim of gaining insights on their biological roles. The selected targets were characterized using glucuronoyl esterase model substrates and with a new synthetic molecule mimicking a putative ester linkage between pectin and lignin. The CE15 enzyme from Phocaeicola vulgatus was structurally determined by X-ray crystallography both with and without carbohydrate ligands with galacturonate binding in a distinct conformation than that of glucuronate. We further explored whether these CE15 enzymes could act akin to pectin methylesterases on pectin-rich biomass but did not find evidence to support the proposed activity. Based on the evidence gathered, the CE15 enzymes in the PULs expected to degrade pectin could be involved in cleavage of uronic acid esters in rhamnogalacturonans.IMPORTANCEThe plant cell wall is a highly complex matrix, and while most of its polymers interact non-covalently, there are also covalent bonds between lignin and carbohydrates. Bonds between xylan and lignin are known, such as the glucuronoyl ester bonds that are cleavable by CE15 enzymes. Our work here indicates that enzymes from CE15 may also have other activities, as we have discovered enzymes in PULs proposed to target other polysaccharides, including pectin. Our study represents the first investigation of such enzymes. Our first hypothesis that the enzymes would act as pectin methylesterases was shown to be false, and we instead propose that they may cleave other esters on complex pectins such as rhamnogalacturonan II. The work presents both the characterization of five novel enzymes and can also provide indirect information about the components of the cell wall itself, which is a highly challenging material to chemically analyze in fine detail.